Detection of clonotypic DNA in the cerebrospinal fluid as a marker of central nervous system invasion in lymphoma.

Diagnosis of parenchymal central nervous system (CNS) invasion and prediction of risk for future CNS recurrence are major challenges in the management of aggressive lymphomas, and accurate biomarkers are needed to supplement clinical risk predictors. For this purpose, we studied a next-generation sequencing (NGS)-based assay that detects tumor-derived DNA for clonotypic immunoglobulin gene rearrangements in the cerebrospinal fluid (CSF) of patients with lymphomas. Used as a diagnostic tool, the NGS-MRD assay detected clonotypic DNA in 100% of CSF samples from 13 patients with known CNS involvement. These included 7 patients with parenchymal brain disease only, whose CSF tested negative by standard cytology and flow cytometry, and 6 historical DNA aliquots collected from patients at median 39 months prior to accession, which had failed to show clonal rearrangements using standard polymerase chain reaction. For risk prognostication, we prospectively collected CSF from 22 patients with newly diagnosed B-cell lymphomas at high clinical risk of CNS recurrence, of whom 8 (36%) had detectable clonotypic DNA in the CSF. Despite intrathecal prophylaxis, a positive NGS-MRD assay in the CSF was associated with 29% cumulative risk of CNS recurrence within 12 months from diagnosis, in contrast with 0% risk among patients with a negative assay (P=0.045). These observations suggest that detection of clonotypic DNA can aid in diagnosis of suspected parenchymal brain recurrence in aggressive lymphoma. Furthermore, the NGS-MRD assay might enhance clinical risk assessment for CNS recurrence among newly diagnosed patients and help select those who might benefit most from novel approaches to CNS-directed prophylaxis.